11-43692293-C-T

Variant names:

• chr11-43692293-C-T
• rs4620711
• NM_016142.3:c.160+11306C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016142.3(HSD17B12):​c.160+11306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,998 control chromosomes in the GnomAD database, including 11,746 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (11746 hom., cov: 32)
• Consequence: HSD17B12 NM_016142.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.21
• Publications: 11 publications found

Genes affected

HSD17B12 (HGNC:18646): (hydroxysteroid 17-beta dehydrogenase 12) This gene encodes a very important 17beta-hydroxysteroid dehydrogenase (17beta-HSD) that converts estrone into estradiol in ovarian tissue. This enzyme is also involved in fatty acid elongation. [provided by RefSeq, Oct 2011]

ENSG00000283341 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSD17B12	NM_016142.3	c.160+11306C>T		intron_variant	Intron 1 of 10	ENST00000278353.10	NP_057226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD17B12	ENST00000278353.10	c.160+11306C>T		intron_variant	Intron 1 of 10	1	NM_016142.3	ENSP00000278353.4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56020 AN: 151880 Hom.: 11734 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.385

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56046 AN: 151998 Hom.: 11746 Cov.: 32 AF XY: 0.377 AC XY: 27979 AN XY: 74290

African (AFR) AF: 0.183 AC: 7580 AN: 41472

American (AMR) AF: 0.529 AC: 8072 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3460

East Asian (EAS) AF: 0.717 AC: 3711 AN: 5174

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4808

European-Finnish (FIN) AF: 0.440 AC: 4641 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27906 AN: 67946

Other (OTH) AF: 0.387 AC: 818 AN: 2112

Alfa AF: 0.401 Hom.: 7236

Bravo AF: 0.368

Asia WGS AF: 0.528 AC: 1828 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.076
DANN	Benign	0.17
PhyloP100		-4.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4620711; hg19: chr11-43713843;